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FCP-INDI / C-PAC

Configurable Pipeline for the Analysis of Connectomes

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✨ BOLD masking steps for `coregistration_prep_fmriprep` (#2014 continued)

shnizzedy opened this issue · comments

commented

Related problem

  • Of the options for func_masking.using

    C-PAC/CPAC/pipeline/schema.py

    Lines 834 to 836 in 1d19541

    ['AFNI', 'FSL', 'FSL_AFNI', 'Anatomical_Refined',
    'Anatomical_Based', 'Anatomical_Resampled',
    'CCS_Anatomical_Refined']
    , before this PR, only FSL_AFNI was compatible with coregistration_prep_fmriprep, and after 1d19541 only FSL_AFNI and CCS_Anatomical_Refined are. I imagine we should make the others compatible as well?

― #2014 (comment)

Proposed feature

For each of the other func_masking.using options ('AFNI', 'FSL', 'Anatomical_Refined', 'Anatomical_Based', and 'Anatomical_Resampled'), we either throw a validation error for coregistration_prep_fmriprep or update the pipeline to work with coregistration_prep_fmriprep paired with any of those options

Acceptance criteria

  • func_masking.using == 'AFNI' + coregistration_prep_fmriprep throws a validation error or runs successfully
  • func_masking.using == 'FSL' + coregistration_prep_fmriprep throws a validation error or runs successfully
  • func_masking.using == 'Anatomical_Refined' + coregistration_prep_fmriprep throws a validation error or runs successfully
  • func_masking.using == 'Anatomical_Based' + coregistration_prep_fmriprep throws a validation error or runs successfully
  • func_masking.using == 'Anatomical_Resampled' + coregistration_prep_fmriprep throws a validation error or runs successfully

Additional context

The nature of the original CCS pipeline (stop and check/choose masks) doesn't fully jive with C-PAC's automated "industrial scale", so we do need to reassess the CCS options at some point based on intended use/strategy.

― #2014 (comment)